[2024-01-24 13:28:19,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference
[2024-01-24 13:28:20,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,660] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg09d9363a-a0f4-4776-9324-2deff32cfb75/GCF_000281175.1_ASM28117v1_genomic.fna.gz | prodigal -d GCF_000281175.1_ASM28117v1_genomic.fna/cds.fna -a GCF_000281175.1_ASM28117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:37,070] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:37,071] [INFO] Task started: HMMsearch
[2024-01-24 13:28:37,071] [INFO] Running command: hmmsearch --tblout GCF_000281175.1_ASM28117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference/reference_markers.hmm GCF_000281175.1_ASM28117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:37,396] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:37,397] [INFO] Found 6/6 markers.
[2024-01-24 13:28:37,441] [INFO] Query marker FASTA was written to GCF_000281175.1_ASM28117v1_genomic.fna/markers.fasta
[2024-01-24 13:28:37,441] [INFO] Task started: Blastn
[2024-01-24 13:28:37,441] [INFO] Running command: blastn -query GCF_000281175.1_ASM28117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference/reference_markers.fasta -out GCF_000281175.1_ASM28117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:38,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:38,147] [INFO] Selected 23 target genomes.
[2024-01-24 13:28:38,148] [INFO] Target genome list was writen to GCF_000281175.1_ASM28117v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:38,158] [INFO] Task started: fastANI
[2024-01-24 13:28:38,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d9363a-a0f4-4776-9324-2deff32cfb75/GCF_000281175.1_ASM28117v1_genomic.fna.gz --refList GCF_000281175.1_ASM28117v1_genomic.fna/target_genomes.txt --output GCF_000281175.1_ASM28117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:55,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:55,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:55,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:55,126] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:55,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:55,126] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Caldilinea aerophila	strain=DSM 14535	GCA_000281175.1	133453	133453	type	True	100.0	1714	1714	95	conclusive
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	76.6581	204	1714	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8725	68	1714	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8173	68	1714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:55,128] [INFO] DFAST Taxonomy check result was written to GCF_000281175.1_ASM28117v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:55,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:55,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:55,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference/checkm_data
[2024-01-24 13:28:55,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:55,178] [INFO] Task started: CheckM
[2024-01-24 13:28:55,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000281175.1_ASM28117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000281175.1_ASM28117v1_genomic.fna/checkm_input GCF_000281175.1_ASM28117v1_genomic.fna/checkm_result
[2024-01-24 13:29:43,348] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:43,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:43,370] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:43,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:43,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000281175.1_ASM28117v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:43,371] [INFO] Task started: Blastn
[2024-01-24 13:29:43,371] [INFO] Running command: blastn -query GCF_000281175.1_ASM28117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b27d8ad-aee5-4cce-b5d6-15eb73c9f5f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000281175.1_ASM28117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:44,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:44,434] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:44,435] [INFO] Target genome list was writen to GCF_000281175.1_ASM28117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:44,499] [INFO] Task started: fastANI
[2024-01-24 13:29:44,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d9363a-a0f4-4776-9324-2deff32cfb75/GCF_000281175.1_ASM28117v1_genomic.fna.gz --refList GCF_000281175.1_ASM28117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000281175.1_ASM28117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:59,271] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:59,286] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:59,287] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000281175.1	s__Caldilinea aerophila	100.0	1714	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	97.04	95.81	0.94	0.92	4	conclusive
GCA_016861025.1	s__Caldilinea sp016861025	78.2061	680	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451595.1	s__Caldilinea sp003451595	77.7013	512	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.85	99.85	0.94	0.94	2	-
GCA_016710365.1	s__Caldilinea sp016710365	77.5324	451	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391565.1	s__Caldilinea sp002391565	77.3841	518	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.77	99.77	0.90	0.90	2	-
GCA_014879855.1	s__Caldilinea sp014879855	76.9983	408	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879975.1	s__Caldilinea sp903879975	76.7313	247	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	98.69	98.69	0.81	0.81	2	-
GCF_006569185.1	s__Litorilinea aerophila	76.6688	202	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_012032975.1	s__JAAUPU01 sp012032975	76.0855	90	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAAUPU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523365.1	s__Bin5 sp011523365	75.6242	62	1714	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:59,288] [INFO] GTDB search result was written to GCF_000281175.1_ASM28117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:59,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:59,292] [INFO] DFAST_QC result json was written to GCF_000281175.1_ASM28117v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:59,292] [INFO] DFAST_QC completed!
[2024-01-24 13:29:59,292] [INFO] Total running time: 0h1m40s